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The San Francisco waterfront institution, Java House on the Embarcadero at Townsend is having rent problems that could force it's closer. August 14, 2007. Lance Iversen/The Chronicle (cq) SUBJECT 8/14/07,in SAN FRANCISCO. CA. MANDATORY CREDIT PHOTOG AND SAN FRANCISCO CHRONICLE/NO SALES MAGS OUT

Photo: By Lance Iversen

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The San Francisco waterfront institution, Java House...

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Pinole Councilman David Cole, in the the soup over an upscale cafe, says he's enlisting at age 38.

Pinole Councilman David Cole, in the the soup over an upscale cafe,...

It's a story we've heard all too often: A little family-run business in a newly gentrified San Francisco neighborhood is suddenly hit with a staggering rent hike by a money-hungry landlord.

Only in this case, the landlord is the Port of San Francisco.

The little business getting jacked is the Java House, a mom-and-pop breakfast and burger joint on Pier 40, just up the street from AT&T Park. It just got served notice that its rent is jumping more than fivefold, from $800 to $4,429 a month, effective this coming Saturday.

"There's no way we can make a go at this rent," said owner PhilPapadopoulos, who along with his wife and daughter has been working the counter for the past 23 years.

Like a lot of waterfront businesses, the Java House is on a month-to-month lease from the port.

And like a lot of waterfront businesses, it was getting a nice deal, paying only $800 a month.

Understandably, the port wanted more. So last year, the port and Papadopoulos worked out a new, 15-year lease, under which the Java House would pay a base of $2,045 a month, plus 7.5 percent of whatever it grossed after rent - with more increases down the road.

The initial figure would total out to about $2,600 a month, based on last year's receipts.

Papadopoulos also agreed to make $300,000 in improvements that the port wanted.

"We kept calling and calling the port and asking what was going on, and they kept telling us, 'Don't worry, don't worry, it's just a formality,' " Papadopoulos said.

The port's Susan Reynolds said her office had a file full of correspondence on negotiations between the port and the Java House since the commission granted initial approval, but that no final lease had been worked out.

In other words, she said, the Port Commission sign-off was only an incremental step, and there were details still to be worked out with the Java House that were never finalized.

Reynolds also said Papadopoulos might have been dragging his feet on the new deal in order to keep paying the $800-a-month rent for as long as possible.

However, when asked to produce anything showing the Java House folks had tried to stall the deal, the port came up empty.

Somewhere along the line, the port decided it could get a lot more money from the Java House. On July 25, it sent Papadopoulos notice that his rent was going up to $4,429 - plus an $8,800 security deposit.

And after Papadopoulos pays the new rent, the port said, negotiations will start on a new lease.

This from a city whose own Small Business Commission touts it as a champion of business friendly policies designed to "support and enhance an environment where small businesses can succeed and flourish."

Right.

Guns 'n' molars:Robert Beckergot quite a fright the other day when he stopped by the World Savings ATM in Castro Valley and found 10 cops in full body armor with assault rifles.

Hostage situation?

Nope - a SWAT team of San Jose cops dispatched to take two prisoners accused of robbing, raping and murdering a woman in San Jose last month to have their teeth checked.

Not just any checkup. The woman was bitten while defending herself, and the suspects were being taken to Dr. John Berke, who does forensic work for Bay Area law enforcement, for a bite analysis.

It's not the first time the cops have visited the doctor with suspects, but it did set a record for firepower.

On the plate: Pinole has long had a reputation as the biggest fast-food stop on I-80, but these days it's nouvelle cuisine that's got the town in an uproar.

At the center of the flap is Pear Street Bistro, an upscale restaurant that - with the help of a $450,000 city-backed redevelopment loan - was supposed to bring some big-city flavor to the gateway to El Sobrante.

The restaurant got into financial trouble and stopped making payments on the loan, and Pinole's politicos and civic bureaucrats found themselves in the soup of the day.

First, the City Council voted to get rid of City Manager Belinda Espinosa, blaming her for the mess.

Now, a citizens group - saying the manager was just a scapegoat - has gathered signatures to have Mayor Maria Alegriaand Councilmen Stephen Tilton and David Colerecalled. They fault Alegria and Cole, in particular, for an all-too-cozy relationship with bistro owner Gary Wong.

One of the food fight highlights: a police memo, cited by the recall group, describing how the allegedly intoxicated mayor mouthed off to a police officer outside the bistro back in January while the cop was issuing a traffic ticket to a restaurant employee.

It all culminated recently with Cole announcing he was taking a leave from the council to join the Army at age 38.

But what really caught our attention was Cole's appearance back in April on KQED-TV's "Check, Please! Bay Area," in which everyday folks are invited to review their favorite restaurants.

Cole chose the Pear Street Bistro, telling show host Leslie Sbrocco: "I would kill for the lobster bisque. ... I can't get enough of it."

To which recall spokesman Jeff Rubin shot back his own review: The food is fair at best, he tells us, "but they charge San Francisco prices."